Characterization of the differentially methylated region of the Impact gene that exhibits Glires-specific imprinting

Comparative genomic analysis of the Impact locus, which is imprinted in Glires but not in other mammals, reveals features required for genomic imprinting

The Lunacy Commission.

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De Novo and Rare Inherited Copy-Number Variations in the Hemiplegic Form of Cerebral Palsy

PurposeHemiplegia is a subtype of cerebral palsy (CP) in which one side of the body is affected. Our earlier study of unselected children with CP demonstrated de novo and clinically relevant rare inherited genomic copy-number variations (CNVs) in 9.6% of participants. Here, we examined the prevalence and types of CNVs specifically in hemiplegic CP.MethodsWe genotyped 97 unrelated probands with hemiplegic CP and their parents. We compared their CNVs to those of 10,851 population controls, in order to identify rare CNVs

Optically stimulated luminescence dating as a geochronological tool for late quaternary sediments in the Red Sea region

This chapter concerns the use of luminescence methods as geochronological tools for dating Late Quaternary sediments in the Red Sea region. The dating methods all use stimulated luminescence to register signals developed in mineral systems in response to long term exposure to ionising radiation in the environment. The principles of luminescence dating are outlined followed by discussion of its application to the Arabian Peninsula, where, particularly in SE Arabia and parts of the interior, a growing corpus of work is emerging, which is helping to define past arid or humid periods of importance to palaeoclimatology and to archaeology. Turning to the Red Sea, studies conducted within the DISPERSE project are presented both in marine and terrestrial settings. The motivation for much of this work concerns definition of the environmental conditions and chronologies for hominin and human dispersion through Arabia. Data are presented which identify, for the first time, late Pleistocene evidence on the inner continental shelf near the Farasan Islands, using material from the 2013 cruise of RV AEGAEO . Results are also presented from the littoral fringe of southwest Saudi Arabia, identifying units associated with MIS5 which have palaeo-environmental and archaeological significance. It is to be hoped that further research in coming decades will continue to extend the regional chronology for the littoral fringe of the Red Sea. In this respect luminescence dating has potential to help define the environmental history of this important area, to assist with assigning marine and terrestrial features into unique stages of Quaternary climate cycles, and to promote better understanding of human-environment interactions in this dynamic area

Physical and genetic analysis of the human chromosome 14 long arm subtelomeric region at 14q32.33 going to 14qter

grantor: University of TorontoThe human immunoglobulin heavy chain gene cluster (IGH) is located at 14q32.33, near the long arm telomere of chromosome 14. Physical maps suggested that 14qter might be some distance from IGH. Human subtelomeric regions are the sites of increased recombination and have a male to female recombination ratio that is higher than elsewhere in the genome. My goal was to complete the map of distal 14q, to develop genetic markers for 14qter, and to examine recombination in this subtelomeric region. Initially, 13 DNA markers were used to characterize naturally occurring terminal deletions, to refine the physical map and determine if deletion breakpoints were near 14qter. Two markers, previously mapped distal to IGH, were mapped proximal to IGH. The breakpoint of a ring chromosome was mapped to a 350 kb interval within IGH, representing the smallest region of distal monosomy 14q reported to date. Somatic cell hybrid lines were next used to map IGH variable region (VH) segments that previously were not placed within IGH. Four NotI DNA fragments, representing eleven VH segments, mapped to chromosomes 15 and 16. Two yeast artificial chromosomes (YAC) containing functional human telomeres were mapped to the telomeric end of IGH. A VH segment at the distal ends of the YACs was sensitive to nuclease Bal31 digestion of human DNA, demonstrating that these represent the 14q telomere. The physical map of IGH was completed and extends to within 25 kb of the telomere. Polymorphic markers were cloned from the distal part of IGH, approximately 90 and 200 kb from the telomere. Haplotypes of these markers were constructed for use as a highly polymorphic genetic marker which will be useful for anchoring genetic maps. Linkage analysis using the 40 pedigree CEPH reference panel revealed increased recombination within this region. Recombination was not significantly higher in males than in females, indicating that this region differs from other human subtelomeric regions.Ph.D

Characterization of the differentially methylated region of the Impactgene that exhibits Glires-specific imprinting

Abstract Background Imprinted genes are exclusively expressed from one of the two parental alleles in a parent-of-origin-specific manner. In mammals, nearly 100 genes are documented to be imprinted. To understand the mechanism behind this gene regulation and to identify novel imprinted genes, common features of DNA sequences have been analyzed; however, the general features required for genomic imprinting have not yet been identified, possibly due to variability in underlying molecular mechanisms from locus to locus. Results We performed a thorough comparative genomic analysis of a single locus, Impact, which is imprinted only in Glires (rodents and lagomorphs). The fact that Glires and primates diverged from each other as recent as 70 million years ago makes comparisons between imprinted and non-imprinted orthologues relatively reliable. In species from the Glires clade, Impact bears a differentially methylated region, whereby the maternal allele is hypermethylated. Analysis of this region demonstrated that imprinting was not associated with the presence of direct tandem repeats nor with CpG dinucleotide density. In contrast, a CpG periodicity of 8 bp was observed in this region in species of the Glires clade compared to those of carnivores, artiodactyls, and primates. Conclusions We show that tandem repeats are dispensable, establishment of the differentially methylated region does not rely on G+C content and CpG density, and the CpG periodicity of 8 bp is meaningful to the imprinting. This interval has recently been reported to be optimal for de novo methylation by the Dnmt3a-Dnmt3L complex, suggesting its importance in the establishment of imprinting in Impact and other genes

Mutational Landscape of Autism Spectrum Disorder Brain Tissue

Rare post-zygotic mutations in the brain are now known to contribute to several neurodevelopmental disorders, including autism spectrum disorder (ASD). However, due to the limited availability of brain tissue, most studies rely on estimates of mosaicism from peripheral samples. In this study, we undertook whole exome sequencing on brain tissue from 26 ASD brain donors from the Harvard Brain Tissue Resource Center (HBTRC) and ascertained the presence of post-zygotic and germline mutations categorized as pathological, including those impacting known ASD-implicated genes. Although quantification did not reveal enrichment for post-zygotic mutations compared with the controls (n = 15), a small number of pathogenic, potentially ASD-implicated mutations were identified, notably in TRAK1 and CLSTN3. Furthermore, germline mutations were identified in the same tissue samples in several key ASD genes, including PTEN, SC1A, CDH13, and CACNA1C. The establishment of tissue resources that are available to the scientific community will facilitate the discovery of new mutations for ASD and other neurodevelopmental disorders